nt2aa.py

#!/usr/bin/env python3
# nt2aa
# SK


def nt2aa(nucleotides, allow_uracil=True, allow_stop_codon=False):
    '''Returns amino acid translation for a nucleotide sequence of triplets, and None otherwise
    '''

    if not len(nucleotides)%3 == 0:
        return None

    triplets = {
            'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
            'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
            'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
            'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
            'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
            'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
            'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
            'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
            'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
            'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
            'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
            'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
            'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
            'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
            'TAC':'Y', 'TAT':'Y', 'TAA':'*', 'TAG':'*',
            'TGC':'C', 'TGT':'C', 'TGA':'*', 'TGG':'W'
        }

    if allow_uracil:
        nucleotides.replace('U', 'T')

    peptide = ""
    for pos in range(0, len(nucleotides), 3):
        codon = nucleotides[pos:pos+3]
        peptide += triplets[codon]

    # stop codon
    if '*' in peptide:
        return None
    
    return peptide